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- EMDB-13544: HsPepT2 bound to Ala-Phe in the inward facing partially occluded ... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-13544
TitleHsPepT2 bound to Ala-Phe in the inward facing partially occluded conformation
Map datapost processed in Phenix. Used for refinement
Sample
  • Complex: Human PepT2
    • Complex: ALA-PHE
      • Protein or peptide: ALA-PHE
    • Protein or peptide: Solute carrier family 15 member 2
Function / homology
Function and homology information


dipeptide transport / peptidoglycan transport / Proton/oligopeptide cotransporters / dipeptide import across plasma membrane / peptide:proton symporter activity / dipeptide transmembrane transporter activity / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / xenobiotic detoxification by transmembrane export across the plasma membrane / xenobiotic transport / renal absorption ...dipeptide transport / peptidoglycan transport / Proton/oligopeptide cotransporters / dipeptide import across plasma membrane / peptide:proton symporter activity / dipeptide transmembrane transporter activity / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / xenobiotic detoxification by transmembrane export across the plasma membrane / xenobiotic transport / renal absorption / transport across blood-brain barrier / monoatomic ion transport / protein transport / apical plasma membrane / innate immune response / extracellular exosome / plasma membrane
Similarity search - Function
Oligopeptide transporter / PTR2 family proton/oligopeptide symporters signature 1. / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Alpha/beta knot methyltransferases / MFS transporter superfamily
Similarity search - Domain/homology
Solute carrier family 15 member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsKiller M / Wald J / Pieprzyk J / Marlovits TC / Loew C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2021
Title: Structural snapshots of human PepT1 and PepT2 reveal mechanistic insights into substrate and drug transport across epithelial membranes.
Authors: Maxime Killer / Jiri Wald / Joanna Pieprzyk / Thomas C Marlovits / Christian Löw /
Abstract: The uptake of peptides in mammals plays a crucial role in nutrition and inflammatory diseases. This process is mediated by promiscuous transporters of the solute carrier family 15, which form part of ...The uptake of peptides in mammals plays a crucial role in nutrition and inflammatory diseases. This process is mediated by promiscuous transporters of the solute carrier family 15, which form part of the major facilitator superfamily. Besides the uptake of short peptides, peptide transporter 1 (PepT1) is a highly abundant drug transporter in the intestine and represents a major route for oral drug delivery. PepT2 also allows renal drug reabsorption from ultrafiltration and brain-to-blood efflux of neurotoxic compounds. Here, we present cryogenic electron microscopy (cryo-EM) structures of human PepT1 and PepT2 captured in four different states throughout the transport cycle. The structures reveal the architecture of human peptide transporters and provide mechanistic insights into substrate recognition and conformational transitions during transport. This may support future drug design efforts to increase the bioavailability of different drugs in the human body.
History
DepositionSep 4, 2021-
Header (metadata) releaseOct 20, 2021-
Map releaseOct 20, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pmy
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13544.png

Downloads & links

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Map

FileDownload / File: emd_13544.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost processed in Phenix. Used for refinement
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 6.0 / Movie #1: 6
Minimum - Maximum-25.424635 - 43.631298
Average (Standard dev.)5.020144e-12 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z217.600217.600217.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-25.42543.6310.000

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Supplemental data

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Mask #1

Fileemd_13544_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_13544_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_13544_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13544_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human PepT2

EntireName: Human PepT2
Components
  • Complex: Human PepT2
    • Complex: ALA-PHE
      • Protein or peptide: ALA-PHE
    • Protein or peptide: Solute carrier family 15 member 2

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Supramolecule #1: Human PepT2

SupramoleculeName: Human PepT2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #2: ALA-PHE

SupramoleculeName: ALA-PHE / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: synthetic construct (others)

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Macromolecule #1: Solute carrier family 15 member 2

MacromoleculeName: Solute carrier family 15 member 2 / type: protein_or_peptide / ID: 1 / Details: HsPepT2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.861125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNPFQKNESK ETLFSPVSIE EVPPRPPSPP KKPSPTICGS NYPLSIAFIV VNEFCERFSY YGMKAVLILY FLYFLHWNED TSTSIYHAF SSLCYFTPIL GAAIADSWLG KFKTIIYLSL VYVLGHVIKS LGALPILGGQ VVHTVLSLIG LSLIALGTGG I KPCVAAFG ...String:
MNPFQKNESK ETLFSPVSIE EVPPRPPSPP KKPSPTICGS NYPLSIAFIV VNEFCERFSY YGMKAVLILY FLYFLHWNED TSTSIYHAF SSLCYFTPIL GAAIADSWLG KFKTIIYLSL VYVLGHVIKS LGALPILGGQ VVHTVLSLIG LSLIALGTGG I KPCVAAFG GDQFEEKHAE ERTRYFSVFY LSINAGSLIS TFITPMLRGD VQCFGEDCYA LAFGVPGLLM VIALVVFAMG SK IYNKPPP EGNIVAQVFK CIWFAISNRF KNRSGDIPKR QHWLDWAAEK YPKQLIMDVK ALTRVLFLYI PLPMFWALLD QQG SRWTLQ AIRMNRNLGF FVLQPDQMQV LNPLLVLIFI PLFDFVIYRL VSKCGINFSS LRKMAVGMIL ACLAFAVAAA VEIK INEMA PAQPGPQEVF LQVLNLADDE VKVTVVGNEN NSLLIESIKS FQKTPHYSKL HLKTKSQDFH FHLKYHNLSL YTEHS VQEK NWYSLVIRED GNSISSMMVK DTESRTTNGM TTVRFVNTLH KDVNISLSTD TSLNVGEDYG VSAYRTVQRG EYPAVH CRT EDKNFSLNLG LLDFGAAYLF VITNNTNQGL QAWKIEDIPA NKMSIAWQLP QYALVTAGEV MFSVTGLEFS YSQAPSS MK SVLQAAWLLT IAVGNIIVLV VAQFSGLVQW AEFILFSCLL LVICLIFSIM GYYYVPVKTE DMRGPADKHI PHIQGNMI K LETKKTKL

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Macromolecule #2: ALA-PHE

MacromoleculeName: ALA-PHE / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 236.267 Da
SequenceString:
AF

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: PROPANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 81.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 454149
FSC plot (resolution estimation)

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